Their second-half goals followed a soporific first half played in front of a subdued crowd at a half-empty stadium.
Muntari broke the deadlock 10 minutes after the break, meeting a Chievo clearance just outside the penalty area with a dipping left-foot volley which flew in under the bar.
Honda made the game safe in the 78th when he curled a 30-metre free kick around the wall for his fourth league goal of the season.
There were 36 fouls in the stop-start game, Milan gave away possession far too often and only kept a clean sheet thanks to the limitations of their opponents, who have lost four of their six games.
Milan have 11 points from six matches, four behind leading pair Juventus and AS Roma who meet on Sunday (5 p.m. BST).
Verona also have 11 points after an 89th minute goal from Panagiotis Tachtsidis gave them a 1-0 win over Cagliari, who were unable to repeat the performance which saw them win 4-1 at Inter Milan a week ago.
(Writing by Brian Homewood; Editing by Ken Ferris)
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